1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
|
global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
MFD MFD '(2S,3S,8S,9S)-3-AMINO-9-METHOXY-2,6,' non-polymer 52 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MFD
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
MFD OXT O OC -0.500 0.000 0.000 0.000
MFD C1 C C 0.000 -1.010 -0.299 0.676
MFD O1 O OC -0.500 -0.920 -1.144 1.594
MFD C2 C CH1 0.000 -2.334 0.360 0.386
MFD H2 H H 0.000 -2.239 1.447 0.517
MFD CM2 C CH3 0.000 -2.750 0.054 -1.054
MFD HM23 H H 0.000 -3.681 0.517 -1.259
MFD HM22 H H 0.000 -2.017 0.427 -1.721
MFD HM21 H H 0.000 -2.842 -0.994 -1.181
MFD C3 C CH1 0.000 -3.394 -0.178 1.348
MFD H3 H H 0.000 -3.489 -1.265 1.218
MFD N3 N NH2 0.000 -2.994 0.115 2.731
MFD HN32 H H 0.000 -2.086 0.520 2.925
MFD HN31 H H 0.000 -3.623 -0.086 3.499
MFD C4 C C1 0.000 -4.718 0.479 1.058
MFD H4 H H 0.000 -4.816 1.549 1.135
MFD C5 C C1 0.000 -5.764 -0.258 0.707
MFD H5 H H 0.000 -5.666 -1.328 0.630
MFD C6 C C 0.000 -7.057 0.384 0.423
MFD CM6 C CH3 0.000 -7.193 1.881 0.532
MFD HM63 H H 0.000 -6.889 2.196 1.497
MFD HM62 H H 0.000 -6.582 2.347 -0.198
MFD HM61 H H 0.000 -8.203 2.158 0.374
MFD C7 C C1 0.000 -8.103 -0.354 0.071
MFD H7 H H 0.000 -8.029 -1.428 0.076
MFD C8 C CH1 0.000 -9.392 0.311 -0.335
MFD H8 H H 0.000 -9.238 1.397 -0.407
MFD CM8 C CH3 0.000 -9.840 -0.231 -1.694
MFD HM83 H H 0.000 -10.747 0.236 -1.980
MFD HM82 H H 0.000 -9.095 -0.028 -2.419
MFD HM81 H H 0.000 -9.990 -1.278 -1.626
MFD C9 C CH1 0.000 -10.470 0.019 0.711
MFD H9 H H 0.000 -10.098 0.298 1.707
MFD O9 O O2 0.000 -10.784 -1.375 0.694
MFD CM9 C CH3 0.000 -10.512 -1.877 2.003
MFD HM93 H H 0.000 -9.475 -1.797 2.204
MFD HM92 H H 0.000 -11.055 -1.314 2.717
MFD HM91 H H 0.000 -10.805 -2.893 2.060
MFD "C'" C CH2 0.000 -11.726 0.828 0.390
MFD "H'1" H H 0.000 -12.094 0.551 -0.600
MFD "H'2" H H 0.000 -11.485 1.893 0.402
MFD "C1'" C CR6 0.000 -12.787 0.540 1.421
MFD "C2'" C CR16 0.000 -12.864 1.309 2.566
MFD "H2'" H H 0.000 -12.163 2.118 2.724
MFD "C3'" C CR16 0.000 -13.838 1.044 3.511
MFD "H3'" H H 0.000 -13.899 1.647 4.409
MFD "C6'" C CR16 0.000 -13.687 -0.490 1.218
MFD "H6'" H H 0.000 -13.631 -1.087 0.316
MFD "C5'" C CR16 0.000 -14.657 -0.757 2.164
MFD "H5'" H H 0.000 -15.357 -1.568 2.008
MFD "C4'" C CR16 0.000 -14.734 0.011 3.310
MFD "H4'" H H 0.000 -15.495 -0.197 4.052
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
MFD OXT n/a C1 START
MFD C1 OXT C2 .
MFD O1 C1 . .
MFD C2 C1 C3 .
MFD H2 C2 . .
MFD CM2 C2 HM21 .
MFD HM23 CM2 . .
MFD HM22 CM2 . .
MFD HM21 CM2 . .
MFD C3 C2 C4 .
MFD H3 C3 . .
MFD N3 C3 HN31 .
MFD HN32 N3 . .
MFD HN31 N3 . .
MFD C4 C3 C5 .
MFD H4 C4 . .
MFD C5 C4 C6 .
MFD H5 C5 . .
MFD C6 C5 C7 .
MFD CM6 C6 HM61 .
MFD HM63 CM6 . .
MFD HM62 CM6 . .
MFD HM61 CM6 . .
MFD C7 C6 C8 .
MFD H7 C7 . .
MFD C8 C7 C9 .
MFD H8 C8 . .
MFD CM8 C8 HM81 .
MFD HM83 CM8 . .
MFD HM82 CM8 . .
MFD HM81 CM8 . .
MFD C9 C8 "C'" .
MFD H9 C9 . .
MFD O9 C9 CM9 .
MFD CM9 O9 HM91 .
MFD HM93 CM9 . .
MFD HM92 CM9 . .
MFD HM91 CM9 . .
MFD "C'" C9 "C1'" .
MFD "H'1" "C'" . .
MFD "H'2" "C'" . .
MFD "C1'" "C'" "C6'" .
MFD "C2'" "C1'" "C3'" .
MFD "H2'" "C2'" . .
MFD "C3'" "C2'" "H3'" .
MFD "H3'" "C3'" . .
MFD "C6'" "C1'" "C5'" .
MFD "H6'" "C6'" . .
MFD "C5'" "C6'" "C4'" .
MFD "H5'" "C5'" . .
MFD "C4'" "C5'" "H4'" .
MFD "H4'" "C4'" . END
MFD "C4'" "C3'" . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
MFD N3 C3 single 1.450 0.020
MFD HN31 N3 single 1.010 0.020
MFD HN32 N3 single 1.010 0.020
MFD C2 C1 single 1.500 0.020
MFD C3 C2 single 1.524 0.020
MFD CM2 C2 single 1.524 0.020
MFD H2 C2 single 1.099 0.020
MFD O1 C1 deloc 1.250 0.020
MFD C1 OXT deloc 1.250 0.020
MFD C4 C3 single 1.510 0.020
MFD H3 C3 single 1.099 0.020
MFD HM21 CM2 single 1.059 0.020
MFD HM22 CM2 single 1.059 0.020
MFD HM23 CM2 single 1.059 0.020
MFD C7 C6 double 1.340 0.020
MFD C8 C7 single 1.510 0.020
MFD H7 C7 single 1.077 0.020
MFD C6 C5 single 1.475 0.020
MFD CM6 C6 single 1.500 0.020
MFD C5 C4 double 1.330 0.020
MFD H5 C5 single 1.077 0.020
MFD H4 C4 single 1.077 0.020
MFD "C'" C9 single 1.524 0.020
MFD "C1'" "C'" single 1.511 0.020
MFD "H'1" "C'" single 1.092 0.020
MFD "H'2" "C'" single 1.092 0.020
MFD C9 C8 single 1.524 0.020
MFD O9 C9 single 1.426 0.020
MFD H9 C9 single 1.099 0.020
MFD CM8 C8 single 1.524 0.020
MFD H8 C8 single 1.099 0.020
MFD "C4'" "C3'" double 1.390 0.020
MFD "C4'" "C5'" single 1.390 0.020
MFD "H4'" "C4'" single 1.083 0.020
MFD "C3'" "C2'" single 1.390 0.020
MFD "H3'" "C3'" single 1.083 0.020
MFD "C2'" "C1'" double 1.390 0.020
MFD "H2'" "C2'" single 1.083 0.020
MFD "C6'" "C1'" single 1.390 0.020
MFD "C5'" "C6'" double 1.390 0.020
MFD "H6'" "C6'" single 1.083 0.020
MFD "H5'" "C5'" single 1.083 0.020
MFD CM9 O9 single 1.426 0.020
MFD HM91 CM9 single 1.059 0.020
MFD HM92 CM9 single 1.059 0.020
MFD HM93 CM9 single 1.059 0.020
MFD HM81 CM8 single 1.059 0.020
MFD HM82 CM8 single 1.059 0.020
MFD HM83 CM8 single 1.059 0.020
MFD HM61 CM6 single 1.059 0.020
MFD HM62 CM6 single 1.059 0.020
MFD HM63 CM6 single 1.059 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
MFD OXT C1 O1 123.000 3.000
MFD OXT C1 C2 118.500 3.000
MFD O1 C1 C2 118.500 3.000
MFD C1 C2 H2 108.810 3.000
MFD C1 C2 CM2 109.470 3.000
MFD C1 C2 C3 109.470 3.000
MFD H2 C2 CM2 108.340 3.000
MFD H2 C2 C3 108.340 3.000
MFD CM2 C2 C3 111.000 3.000
MFD C2 CM2 HM23 109.470 3.000
MFD C2 CM2 HM22 109.470 3.000
MFD C2 CM2 HM21 109.470 3.000
MFD HM23 CM2 HM22 109.470 3.000
MFD HM23 CM2 HM21 109.470 3.000
MFD HM22 CM2 HM21 109.470 3.000
MFD C2 C3 H3 108.340 3.000
MFD C2 C3 N3 109.470 3.000
MFD C2 C3 C4 109.470 3.000
MFD H3 C3 N3 109.470 3.000
MFD H3 C3 C4 108.810 3.000
MFD N3 C3 C4 109.470 3.000
MFD C3 N3 HN32 120.000 3.000
MFD C3 N3 HN31 120.000 3.000
MFD HN32 N3 HN31 120.000 3.000
MFD C3 C4 H4 120.000 3.000
MFD C3 C4 C5 120.000 3.000
MFD H4 C4 C5 120.000 3.000
MFD C4 C5 H5 120.000 3.000
MFD C4 C5 C6 120.000 3.000
MFD H5 C5 C6 120.000 3.000
MFD C5 C6 CM6 120.000 3.000
MFD C5 C6 C7 120.000 3.000
MFD CM6 C6 C7 120.000 3.000
MFD C6 CM6 HM63 109.470 3.000
MFD C6 CM6 HM62 109.470 3.000
MFD C6 CM6 HM61 109.470 3.000
MFD HM63 CM6 HM62 109.470 3.000
MFD HM63 CM6 HM61 109.470 3.000
MFD HM62 CM6 HM61 109.470 3.000
MFD C6 C7 H7 120.000 3.000
MFD C6 C7 C8 120.500 3.000
MFD H7 C7 C8 120.000 3.000
MFD C7 C8 H8 108.810 3.000
MFD C7 C8 CM8 109.470 3.000
MFD C7 C8 C9 109.470 3.000
MFD H8 C8 CM8 108.340 3.000
MFD H8 C8 C9 108.340 3.000
MFD CM8 C8 C9 111.000 3.000
MFD C8 CM8 HM83 109.470 3.000
MFD C8 CM8 HM82 109.470 3.000
MFD C8 CM8 HM81 109.470 3.000
MFD HM83 CM8 HM82 109.470 3.000
MFD HM83 CM8 HM81 109.470 3.000
MFD HM82 CM8 HM81 109.470 3.000
MFD C8 C9 H9 108.340 3.000
MFD C8 C9 O9 109.470 3.000
MFD C8 C9 "C'" 111.000 3.000
MFD H9 C9 O9 109.470 3.000
MFD H9 C9 "C'" 108.340 3.000
MFD O9 C9 "C'" 109.470 3.000
MFD C9 O9 CM9 111.800 3.000
MFD O9 CM9 HM93 109.470 3.000
MFD O9 CM9 HM92 109.470 3.000
MFD O9 CM9 HM91 109.470 3.000
MFD HM93 CM9 HM92 109.470 3.000
MFD HM93 CM9 HM91 109.470 3.000
MFD HM92 CM9 HM91 109.470 3.000
MFD C9 "C'" "H'1" 109.470 3.000
MFD C9 "C'" "H'2" 109.470 3.000
MFD C9 "C'" "C1'" 109.470 3.000
MFD "H'1" "C'" "H'2" 107.900 3.000
MFD "H'1" "C'" "C1'" 109.470 3.000
MFD "H'2" "C'" "C1'" 109.470 3.000
MFD "C'" "C1'" "C2'" 120.000 3.000
MFD "C'" "C1'" "C6'" 120.000 3.000
MFD "C2'" "C1'" "C6'" 120.000 3.000
MFD "C1'" "C2'" "H2'" 120.000 3.000
MFD "C1'" "C2'" "C3'" 120.000 3.000
MFD "H2'" "C2'" "C3'" 120.000 3.000
MFD "C2'" "C3'" "H3'" 120.000 3.000
MFD "C2'" "C3'" "C4'" 120.000 3.000
MFD "H3'" "C3'" "C4'" 120.000 3.000
MFD "C1'" "C6'" "H6'" 120.000 3.000
MFD "C1'" "C6'" "C5'" 120.000 3.000
MFD "H6'" "C6'" "C5'" 120.000 3.000
MFD "C6'" "C5'" "H5'" 120.000 3.000
MFD "C6'" "C5'" "C4'" 120.000 3.000
MFD "H5'" "C5'" "C4'" 120.000 3.000
MFD "C5'" "C4'" "H4'" 120.000 3.000
MFD "C5'" "C4'" "C3'" 120.000 3.000
MFD "H4'" "C4'" "C3'" 120.000 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
MFD var_1 OXT C1 C2 C3 -179.947 20.000 3
MFD var_2 C1 C2 CM2 HM21 60.036 20.000 3
MFD var_3 C1 C2 C3 C4 -179.949 20.000 3
MFD var_4 C2 C3 N3 HN31 173.805 20.000 1
MFD var_5 C2 C3 C4 C5 120.000 20.000 1
MFD CONST_1 C3 C4 C5 C6 179.990 0.000 0
MFD var_6 C4 C5 C6 C7 179.936 20.000 1
MFD var_7 C5 C6 CM6 HM61 -175.277 20.000 1
MFD CONST_2 C5 C6 C7 C8 -174.674 0.000 0
MFD var_8 C6 C7 C8 C9 -112.496 20.000 1
MFD var_9 C7 C8 CM8 HM81 60.008 20.000 3
MFD var_10 C7 C8 C9 "C'" 173.199 20.000 3
MFD var_11 C8 C9 O9 CM9 120.915 20.000 1
MFD var_12 C9 O9 CM9 HM91 175.497 20.000 1
MFD var_13 C8 C9 "C'" "C1'" 179.988 20.000 3
MFD var_14 C9 "C'" "C1'" "C6'" -90.345 20.000 2
MFD CONST_3 "C'" "C1'" "C2'" "C3'" 180.000 0.000 0
MFD CONST_4 "C1'" "C2'" "C3'" "C4'" 0.000 0.000 0
MFD CONST_5 "C'" "C1'" "C6'" "C5'" 180.000 0.000 0
MFD CONST_6 "C1'" "C6'" "C5'" "C4'" 0.000 0.000 0
MFD CONST_7 "C6'" "C5'" "C4'" "C3'" 0.000 0.000 0
MFD CONST_8 "C5'" "C4'" "C3'" "C2'" 0.000 0.000 0
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
MFD chir_01 C2 C1 C3 CM2 positiv
MFD chir_02 C3 N3 C2 C4 positiv
MFD chir_03 C9 "C'" C8 O9 positiv
MFD chir_04 C8 C7 C9 CM8 positiv
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
MFD plan-1 N3 0.020
MFD plan-1 C3 0.020
MFD plan-1 HN31 0.020
MFD plan-1 HN32 0.020
MFD plan-2 C1 0.020
MFD plan-2 C2 0.020
MFD plan-2 O1 0.020
MFD plan-2 OXT 0.020
MFD plan-3 C7 0.020
MFD plan-3 C6 0.020
MFD plan-3 C8 0.020
MFD plan-3 H7 0.020
MFD plan-3 C5 0.020
MFD plan-3 CM6 0.020
MFD plan-3 H5 0.020
MFD plan-4 C5 0.020
MFD plan-4 C6 0.020
MFD plan-4 C4 0.020
MFD plan-4 H5 0.020
MFD plan-4 C3 0.020
MFD plan-4 H4 0.020
MFD plan-5 "C4'" 0.020
MFD plan-5 "C3'" 0.020
MFD plan-5 "C5'" 0.020
MFD plan-5 "H4'" 0.020
MFD plan-5 "C2'" 0.020
MFD plan-5 "C1'" 0.020
MFD plan-5 "C6'" 0.020
MFD plan-5 "H3'" 0.020
MFD plan-5 "H2'" 0.020
MFD plan-5 "C'" 0.020
MFD plan-5 "H6'" 0.020
MFD plan-5 "H5'" 0.020
# ------------------------------------------------------
|
